36种黄精属植物叶绿体基因组密码子使用偏好性分析

LI Hong; ZHOU Meng-li; WANG Xia; GUO Lei; WANG Rui-hong

doi:10.3969/j.issn.1009-7791.2025.05.002

亚热带植物科学 >

2025 , Vol. 54 >Issue 5: 497 - 507

DOI: https://doi.org/10.3969/j.issn.1009-7791.2025.05.002

研究论文

36种黄精属植物叶绿体基因组密码子使用偏好性分析

LI Hong ,
ZHOU Meng-li ,
WANG Xia ,
GUO Lei ,
WANG Rui-hong

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(浙江理工大学生命科学与医药学院，浙江杭州 310018)

收稿日期: 2025-04-30

录用日期: 2025-07-30

网络出版日期: 2025-12-17

基金资助

国家自然科学基金(31600183)；浙江省基础公益研究计划(LGN22H280005)；浙江理工大学基本科研业务费(24042128-Y)；浙江省“尖兵”“领雁”研发攻关计划(2023C02017)

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Codon Usage Bias in the Chloroplast Genomes of 36 Polygonatum Species

李红，周梦丽，王霞，郭蕾，王瑞红

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(College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, Zhejiang China)

Received date: 2025-04-30

Accepted date: 2025-07-30

Online published: 2025-12-17

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摘要

为探究黄精属Polygonatum药用植物叶绿体基因组密码子的使用偏好性及其影响因素，利用CodonW 1.4.2、CUSP以及SPSS27等软件对36种黄精属植物叶绿体基因组蛋白质编码序列(CDS)进行密码子偏好性分析。结果表明，有效密码子数在48.32～48.57之间，密码子适应指数在0.166～0.168之间，说明黄精属植物叶绿体基因组密码子偏好性较弱；36个黄精属物种确定了5个共有的最优密码子，分别为UUU、CUU、ACA、CAA、GGA，都偏好以A/U结尾。36种黄精属植物的密码子偏好性主要受到自然选择的影响。研究结果为黄精属药用植物遗传育种、种质资源保护等研究提供理论依据。

关键词： 黄精属; 叶绿体基因组; 密码子偏好性; 最优密码子; 自然选择

本文引用格式

LI Hong , ZHOU Meng-li , WANG Xia , GUO Lei , WANG Rui-hong . 36种黄精属植物叶绿体基因组密码子使用偏好性分析[J]. 亚热带植物科学, 2025 , 54(5) : 497 -507 . DOI: 10.3969/j.issn.1009-7791.2025.05.002

Abstract

In order to explore the bias of the use of codons and and its influencing factors in the chloroplast genome of Polygonatum medicinal plants, CodonW 1.4.2, CUSP and SPSS27 were used to analyze the codon bias of 36 Polygonatum species. The results showed that the effective number of codons (ENC) ranges between 48.32 and 48.57, and the codon adaptation index (CAI) ranges between 0.166 and 0.168, indicating that the codon preference of the chloroplast genome of Polygonatum was weak. The 36 species of Polygonatum identified five common optimal codons, namely UUU, CUU, ACA, CAA and GGA, which all preferred to end with A/U nucleotides. The codon bias of 36 species of Polygonatum was mainly affected by natural selection. The results provide a theoretical basis for the genetic breeding and germplasm resources protection of Polygonatum medicinal plants.

Key words： Polygonatum; chloroplast genome; codon usage bias; optimal codon; natural selection

参考文献

[1] Zhao P, Zhao C, Li X, Gao Q, Huang L, Xiao P, Gao W. The genus Polygonatum: a review of ethnopharmacology, phytochemistry andpharmacology [J]. Journal of Ethnopharmacology, 2018, 214: 274–291.
[2] Liu D, Tang W, Han C, Nie S. Advances in Polygonatum sibiricum polysaccharides: Extraction, purification, structure, biosynthesis, and bioactivity [J]. Frontiers in Nutrition, 2022, 9: 1074671.
[3] 崔阔澍, 肖特, 李慧萍, Khan A, Bawa G, 陈国鹏, 彭腾, 李斌, 杨文钰, 郑本川, 吴茂力, 詹志来. 我国黄精种质资源研究进展[J]. 江苏农业科学, 2021, 49(11): 35–39.
[4] Cui X, Wang S, Cao H, Guo H, Li Y, Xu F, Zheng M, Xi X, Han C. A review: the bioactivities and pharmacological applications of Polygonatum sibiricum polysaccharides [J]. Molecules, 2018, 23(5): 1170.
[5] 刘爽, 胡舒婷, 贾巧君, 梁宗锁.黄精的化学组成及药理作用的研究进展[J]. 天然产物研究与开发, 2021, 33(10): 1783–1796.
[6] Liu R, Zhang X, Cai Y, Xu S, Xu Q, Ling C, Li X, Li W, Liu P, Liu W. Research progress on medicinal components and pharmacological activities of Polygonatum sibiricum [J]. Journal of Ethnopharmacology, 2024, 328:118024.
[7] Zhao X, Patil S, Qian A, Zhao C. Bioactive compounds of Polygonatum sibiricum – therapeutic effect and biological activity [J]. Endocr Metab Immune Disord Drug Targets, 2022, 22(1): 26–37.
[8] Chinese Pharmacopoeia Commission. Pharmacopoeia of the people's Republic of China: Vol I [M]. Beijing: China Medical Science Press, 2020: 319–320.
[9] 郭英纯. 浅述黄精价值及林下种植技术[J]. 农村经济与科技, 2021, 32(18): 55–57.
[10] 阙灵, 杨光, 李颖, 单锋, 陈敏, 黄璐琦. 《既是食品又是药品的物品名单》修订概况[J]. 中国药学杂志, 2017, 52(7): 521–524.
[11] 刘日斌, 钟瑞敏, 朱建华, 刘国凌, 邹秀容, 谢思芸, 叶俊, 孙慧欢. 黄精山药枸杞复合饮料的研制[J]. 食品研究与开发, 2020, 41(19): 140–144.
[12] 王玉良, 陆玮, 刘智慧, 刘国英, 汤有宏. 黄精枸杞酒的有效成分及稳定性研究[J]. 酿酒, 2017, 44(5): 106–109.
[13] Yao H, Li T, Ma Z, Wang X, Xu L, Zhang Y, Cai Y, Tang Z. Codon usage pattern of the ancestor of green plants revealed through Rhodophyta [J]. BMC Genomics, 2023, 24(1):538.
[14] Komar A A. The Yin and Yang of codon usage [J]. Human Molecular Genetics, 2016, 25(R2): R77–R85.
[15] Parvathy S T, Udayasuriyan V, Bhadana V. Codon usage bias [J]. Molecular Biology Reports, 2022, 49(1): 539–565.
[16] Camiolo S, Melito S, Porceddu A. New insights into the interplay between codon bias determinants in plants [J]. DNA Research, 2015, 22(6): 461–470.
[17] Li G, Zhang L, Xue P. Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species [J]. Gene, 2021, 802: 145866.
[18] Chu D, Wei L. Direct in vivo observation of the effect of codon usage bias on gene expression in Arabidopsis hybrids [J]. Journal of Plant Physiology, 2021, 265:153490.
[19] Moss M J, Chamness L M, Clark P L. The effects of codon usage on protein structure and folding [J]. Annual Review of Biophysics, 2024, 53(1): 87–108.
[20] Bae H, Coller J. Codon optimality-mediated mRNA degradation: linking translational elongation to mRNA stability [J]. Molecular Cell, 2022, 82(8): 1467–1476.
[21] Feng L, Zhao G, An M, Wang C, Yin Y. Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species [J]. BMC Genomics, 2023, 24(1): 739.
[22] Niu Y F, Su T, Wu C H, Deng J, Yang F Z. Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships [J]. BMC Genomics, 2023, 24(1): 90.
[23] Li C, Zhou L, Nie J, Wu S, Li W, Liu Y, Liu Y. Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae) [J]. Physiology and Molecular Biology of Plants, 2023, 29(2): 239–251.
[24] Iriarte A, Lamolle G., Musto H. Codon usage bias: an endless tale [J]. Journal of molecular evolution, 2021, 89(9–10): 589–593.
[25] Fages-Lartaud M, Hundvin K, Hohmann-Marriott M F. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii [J]. Plant Journal, 2022, 112(4): 919–945.
[26] Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae [J]. BMC Plant Biology, 2024, 24(1): 424.
[27] Wang Z, Cai Q, Wang Y, Li M, Wang C, Wang Z, Jiao C, Xu C, Wang H, Zhang Z. Comparative analysis of codon bias in the chloroplast genomes of Theaceae species [J]. Frontiers in Genetics, 2022, 13:824610.
[28] Wang Z, Xu B, Li B, Zhou Q, Wang G, Jiang X, Wang C, Xu Z. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species [J]. Peer J, 2020, 8: e8251.
[29] 程文萍, 赵霞, 李依民, 张岗, 颜永刚, 高静, 张明英. 中国特有药用植物距药黄精的叶绿体全基因组解析及黄精属种间系统发育关系分析[J]. 药学学报, 2023, 58(11): 3461–3472.
[30] Kokate P P, Techtmann S M, Werner T. Codon usage bias and dinucleotide preference in 29 Drosophila species [J]. G3-Genes Genomes Genetics, 2021, 11(8): jkab191.
[31] Shen Z, Gan Z, Zhang F, Yi X, Zhang J, Wan X. Analysis of codon usage patterns in Citrus based on coding sequence data [J]. BMC Genomics, 2020, 21(Suppl 5): 234.
[32] Gao M, Huo X, Lu L, Liu M, Zhang G. Analysis of codon usage patterns in Bupleurum falcatum chloroplast genome [J]. Chinese Herbal Medicines, 2023, 15(2): 284–290.
[33] Chakraborty S, Yengkhom S, Uddin A. Analysis of codon usage bias of chloroplast genes in Oryza species: codon usage of chloroplast genes in Oryza species [J]. Planta, 2020, 252(4): 67.
[34] Zhang P, Xu W, Lu X, Wang L. Analysis of codon usage bias of chloroplast genomes in Gynostemma species [J]. Physiology and Molecular Biology of Plants, 2021, 27(12): 2727–2737.
[35] 王晓双, 杨芳, 罗茜, 刘映良, 朱斌. 石斛属叶绿体基因组密码子使用偏性及系统发育分析[J]. 分子植物育种, 2022, 20(23): 7759–7769.
[36] Kawabe A, Miyashita N T. Patterns of codon usage bias in three dicot and four monocot plant species [J]. Genes and Genetic Systems, 2003, 78: 343–352.
[37] Morton B R. Chloroplast DNA codon use: evidence for selection at the psbA locus based on tRNA availability [J]. Journal of Molecular Evolution, 1993, 37(3): 273–280.
[38] Pluhar W. AT2-AT3-Profiling:a new look at synonymous codon usage [J]. Journal of Theoretical Biology, 2006, 243(3): 308–321.
[39] Novoa E M, De Pouplana L M. Speeding with control: codon usage, tRNA, and ribosomes [J]. Trends in Genetics, 2012, 28(11): 574–581.
[40] Liu H, Lu Y, Lan B, Xu J. Codon usage by chloroplast gene is bias in Hemiptelea davidii [J]. Journal of Genetics, 2020, 99(1): 1–11.
[41] Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C. Analysis of codon usage patterns in 48 Aconitum species [J]. BMC Genomics, 2023, 24: 703.
[42] Li T, Ma Z, Ding T, Yang Y, Wang F, Wan X, Liang F, Chen X, Yao H. Codon usage bias and phylogenetic analysis of chloroplast genome in 36 Gracilariaceae species [J]. Funct Integr Genomics, 2024, 24(2): 45.
[43] 赵振宁, 孙浩田, 宋雨茹, 余潇. 山楂属植物叶绿体基因组特征与密码子偏好性分析[J]. 江苏农业学报, 2023, 39(2): 504–517.
[44] 张重菊, 赵懿琛, 赵德刚. 薏苡转录组中密码子使用偏好性分析[J]. 种子, 2022, 41(4): 13–19.
[45] Li G, Pan Z, Gao S, He Y, Xia Q, Jin Y, Yao H. Analysis of synonymous codon usage of chloroplast genome in Porphyraum bilicalis [J]. Genes Genomics, 2019, 41(10):1173–1181.
[46] 原晓龙, 李云琴, 张劲峰, 王毅. 乳油木叶绿体基因组密码子偏好性分析[J]. 分子植物育种, 2020, 18(17): 5658–5664.
[47] 唐玉娟, 赵英, 黄国弟, 付海天, 宋恩亮, 李日旺, 金刚. 芒果叶绿体基因组密码子使用偏好性分析[J]. 热带作物学报, 2021, 42(8): 2143–2150.

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